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<title>Timing analysis for IPMN / PDAC samples</title>

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<h1 class="title toc-ignore">Timing analysis for IPMN / PDAC samples</h1>

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<p>
<strong>Last updated:</strong> 2019-09-17
</p>
<p>
<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 2 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 0
</p>
<p>
<strong>Knit directory:</strong> <code>ipmn-timing/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
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  href="https://github.com/jdblischak/workflowr">workflowr</a> (version 1.4.0.9000). The <em>Checks</em> tab describes the reproducibility checks that were applied when the results were created. The <em>Past versions</em> tab lists the development history.
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabcomrscharpfipmntimingtree1139ea0b016587e237578fcdaad6be200575efa9targetblank1139ea0a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.com/rscharpf/ipmn-timing/tree/1139ea0b016587e237578fcdaad6be200575efa9" target="_blank">1139ea0</a> </a>
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Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated. <br><br> Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
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<pre><code>
Ignored files:
    Ignored:    analysis/.Rhistory
    Ignored:    code/.Rhistory
    Ignored:    code/clock.R
    Ignored:    output/timing.R/
    Ignored:    publish.R

Untracked files:
    Untracked:  code/functions.R
    Untracked:  code/timing.R
    Untracked:  code/timing.sh
    Untracked:  code/timing_master.R
    Untracked:  output/timing_master.R/
    Untracked:  output/timing_summary.Rmd/

Unstaged changes:
    Modified:   analysis/timing_hierarchical.Rmd

</code></pre>
<p>
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
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These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see <code>?wflow_git_remote</code>), click on the hyperlinks in the table below to view them.
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Version
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Author
</th>
<th>
Date
</th>
<th>
Message
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<td>
Rmd
</td>
<td>
<a href="https://gitlab.com/rscharpf/ipmn-timing/blob/1139ea0b016587e237578fcdaad6be200575efa9/analysis/index.Rmd" target="_blank">1139ea0</a>
</td>
<td>
rscharpf
</td>
<td>
2019-09-17
</td>
<td>
add model to timing_summary.rmd
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://glcdn.githack.com/rscharpf/ipmn-timing/raw/c10e0073a0bdfbeb5e406525ab69a326c8d9a7a3/public/index.html" target="_blank">c10e007</a>
</td>
<td>
rscharpf
</td>
<td>
2019-08-28
</td>
<td>
Build site.
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://glcdn.githack.com/rscharpf/ipmn-timing/raw/a32dbed797e83eb45f85a7ac2bad6a52c75309a0/public/index.html" target="_blank">a32dbed</a>
</td>
<td>
rscharpf
</td>
<td>
2019-08-28
</td>
<td>
Host with GitLab.
</td>
</tr>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://gitlab.com/rscharpf/ipmn-timing/blob/290ade5ede503aeb7d342e5c87921398b289e199/analysis/index.Rmd" target="_blank">290ade5</a>
</td>
<td>
rscharpf
</td>
<td>
2019-08-28
</td>
<td>
wflow_publish(c(“analysis/timing_hierarchical.Rmd”,
</td>
</tr>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://gitlab.com/rscharpf/ipmn-timing/blob/0b0a7c62bd560cc738b86d533dcd13c3d0b4a716/analysis/index.Rmd" target="_blank">0b0a7c6</a>
</td>
<td>
rscharpf
</td>
<td>
2019-07-29
</td>
<td>
Start HG IPMN timing project
</td>
</tr>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://gitlab.com/rscharpf/ipmn-timing/blob/37923c159455d9b30ee0247f14804f1cabb0bf30/analysis/index.Rmd" target="_blank">37923c1</a>
</td>
<td>
rscharpf
</td>
<td>
2019-07-25
</td>
<td>
Start workflowr project.
</td>
</tr>
</tbody>
</table>
</div>
<hr>
</div>
</div>
</div>
<div id="project-overview" class="section level1">
<h1>Project overview</h1>
<div id="previous-analyses" class="section level2">
<h2>Previous analyses</h2>
<ol style="list-style-type: decimal">
<li><p><a href="timing.html">Independent Poisson-Gamma models for each patient</a></p></li>
<li><p><a href="timing_hierarchical.html">Hierarchical model to estimate timing for all patients</a></p></li>
</ol>
</div>
</div>
<div id="fit-model-for-each-of-a-range-of-possible-mutation-rates" class="section level1">
<h1>Fit model for each of a range of possible mutation rates</h1>
<ol style="list-style-type: decimal">
<li><a href="timing_summary.html">Hierarchical model to estimate timing for all patients</a></li>
</ol>
</div>


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